Question

Problem with multiple sequence alignment using AlignSeqs

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Nelli • 0

@73578ad0

Last seen 23 months ago

Armenia

Hi,

I have run DADA2 algorithm for my original data and in order to build phylogenetic tree I am trying to perform alignment for v3-4 region of my 19153 unique sequences using this code:

library(DECIPHER)

#Run Sequence Alignment (MSA) using DECIPHER
alignment <- AlignSeqs(DNAStringSet(sequences), anchor=NA)

But it stuck at this alignment step (12 hours have passed):

Aligning Sequences:
================================================================================

Time difference of 193.47 secs

Iteration 1 of 2:

Determining distance matrix based on alignment:
================================================================================

Time difference of 189.15 secs

Reclustering into groups by similarity:
================================================================================

Time difference of 45.95 secs

Realigning Sequences:
================================================================================

Time difference of 149 secs

Iteration 2 of 2:

Determining distance matrix based on alignment:
================================================================================

Time difference of 185.69 secs

Reclustering into groups by similarity:
================================================================================

Time difference of 47.76 secs

Realigning Sequences:
================================================================================

Time difference of 11.27 secs

Refining the alignment:
================================================================================

Time difference of 0.66 secs

I am wondering whether someone can help me to fix this, or if have any other suggestions.

Thanks in advance.

R dada2 DECIPHER • 1.3k views

ADD COMMENT • link updated 2.0 years ago by Erik Wright ▴ 150 • written 2.0 years ago by Nelli • 0

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It is unclear where you are stuck in the output above. It looks like the process finished, because refinement is the last step.

ADD REPLY • link 2.0 years ago Erik Wright ▴ 150

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Yes, but it was on this even after 24 hours. After alignment, it was supposed to save the output as an R object. I thought maybe 19153 is a giant number of sequences for this function.

ADD REPLY • link 2.0 years ago Nelli • 0

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Try this:

alignment <- AlignSeqs(DNAStringSet(sequences), anchor=NA, FUN=function(x, ...) return(x))

Because that will skip the only step that occurs after the progress bar finishes, as in your output above.

ADD REPLY • link 2.0 years ago Erik Wright ▴ 150